---
name: "Bio::Tools::Seg"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Tools::Seg"
---

# Bio::Tools::Seg(3pm)

parse "seg" output

## NAME

Bio::Tools::Seg - parse "seg" output

## SYNOPSIS

```
  use Bio::Tools::Seg;
  my $parser = Bio::Tools::Seg->(-file => 'seg.fasta');
  while ( my $f = $parser->next_result ) {
    if ($f->score < 1.5) {
      print $f->location->to_FTstring, " is low complexity\n";
    }
  }
```

## DESCRIPTION

`"seg"` identifies low-complexity regions on a protein sequence. It is usually part of the `"WU-BLAST"` and `"InterProScan"` packages.

The Bio::Tools::Seg module will only parse the "fasta" output  modes of `"seg"`, i.e. `"seg -l"` (low complexity regions only),  `"seg -h"` (high complexity regions only), or `"seg -a"` (both low  and high).

It creates a Bio::SeqFeature::Generic for each FASTA-like entry  found in the input file. It is up to the user to appropriately filter  these using the feature's score.

## FEEDBACK

### Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list.  Your participation is much appreciated.

```
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
```

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

rather than to the module maintainer directly. Many experienced and  reponsive experts will be able look at the problem and quickly  address it. Please include a thorough description of the problem  with code and data examples if at all possible.

### Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

```
  https://github.com/bioperl/bioperl-live/issues
```

## AUTHOR - Torsten Seemann

Email - torsten.seemann AT infotech.monash.edu.au

## CONTRIBUTOR - Bala

Email - savikalpa@fugu-sg.org

## APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_

### new

```
 Title   : new
 Usage   : my $obj = Bio::Tools::Seg->new();
 Function: Builds a new Bio::Tools::Seg object
 Returns : Bio::Tools::Seg
 Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO
```

### next\_result

```
 Title   : next_result
 Usage   : my $feat = $seg->next_result
 Function: Get the next result set from parser data
 Returns : Bio::SeqFeature::Generic
 Args    : none
```